Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 20 of 129
Found at i:3945707 original size:20 final size:20
Alignment explanation
Indices: 3945678--3945715 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3945668 ATCTTTTTTA
*
3945678 AATTTAAATTTTCTAAATAT
1 AATTTAAATTTTATAAATAT
*
3945698 AATTTTAATTTTATAAAT
1 AATTTAAATTTTATAAAT
3945716 TTTCTAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTAAATTTTATAAATAT
Found at i:3946568 original size:260 final size:260
Alignment explanation
Indices: 3946090--3946572 Score: 641
Period size: 260 Copynumber: 1.9 Consensus size: 260
3946080 AAAAATGTCA
* * *
3946090 AGTTCTACTTGATCAATAATTATAGCTTTGCCATTGACATATGAGATTTTCGTGCTACAATGACC
1 AGTTATACTTGATCAAAAATTATAGCTTTGCCATTAACATATGAGATTTTCGTGCTACAATGACC
* * *
3946155 TCCTTCTAAAATATGCTTTCAAGAGTAATATGTCATATATTAAGTTAGGAGAATTTGAACTTCAA
66 TCCTTCTAAAATATACTTTCAAGAGTAATAGGTCATATATTAAGTTAGGAGAATTAGAACTTCAA
** * * * *
3946220 AATTGAGCATCCTATTAGGCAAAACAATAATTTTATTCGATAAAAATCAATAAAAATTATAATGA
131 AATCAAACATCCCATTAGACAAAACAATAATTTTATTCAATAAAAATCAATAAAAATTATAATGA
*
3946285 TAATATTTAAATATTGCATTTTGTTTAACAAAATTATTGCAGGAAGTAAGAATTGATGTTTGTTT
196 TAATATTTAAATATTACATTTTGTTTAACAAAATTATTGCAGGAAGTAAGAATTGATGTTTGTTT
* * * * * * *
3946350 AGTTATACTTTATCAAAAATTATAGTTTTGTCATTAACTTATGAGATTTTTGTGCTATAATTACC
1 AGTTATACTTGATCAAAAATTATAGCTTTGCCATTAACATATGAGATTTTCGTGCTACAATGACC
* * * * * *
3946415 TCTTTCTAGAATTTACTTTCAAGATTAATAGGTTC-TATTTTATA-TTAGGGGAATTAGAACTTC
66 TCCTTCTAAAATATACTTTCAAGAGTAATAGG-TCATATATTA-AGTTAGGAGAATTAGAACTTC
* * *
3946478 AAAATCAAACATCCCATTAGACAAAACAATAGTTTTA-TCAATTAATAATCAATAAAAGTTATAA
129 AAAATCAAACATCCCATTAGACAAAACAATAATTTTATTCAA-TAAAAATCAATAAAAATTATAA
3946542 T-ATCAATATTTAAATATTACATTTTGTTTAA
193 TGAT-AATATTTAAATATTACATTTTGTTTAA
3946573 TGAGACTATT
Statistics
Matches: 190, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
259 5 0.03
260 182 0.96
261 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (260 bp):
AGTTATACTTGATCAAAAATTATAGCTTTGCCATTAACATATGAGATTTTCGTGCTACAATGACC
TCCTTCTAAAATATACTTTCAAGAGTAATAGGTCATATATTAAGTTAGGAGAATTAGAACTTCAA
AATCAAACATCCCATTAGACAAAACAATAATTTTATTCAATAAAAATCAATAAAAATTATAATGA
TAATATTTAAATATTACATTTTGTTTAACAAAATTATTGCAGGAAGTAAGAATTGATGTTTGTTT
Found at i:3953010 original size:2 final size:2
Alignment explanation
Indices: 3953003--3953029 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3952993 CTTTTCTATG
3953003 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3953030 TTCTGTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3959141 original size:68 final size:67
Alignment explanation
Indices: 3959027--3959160 Score: 157
Period size: 68 Copynumber: 2.0 Consensus size: 67
3959017 TATATCATGT
* * * * *
3959027 AAAATATTAAAATTTATATATTTATATTATATTTTATATAAAAATTATGTGTTATA-ATTTATAT
1 AAAATATTAAAATATAAATATTTATATTATAATTTATATAAAAATTAT-TATTATATATTTAAAT
3959091 TAA
65 TAA
*
3959094 AAAATATATAAAATATAAATATTTAT-TTATTAAATTTATAT-ATAATTATTATTATATATTTAA
1 AAAATAT-TAAAATATAAATATTTATATTA-T-AATTTATATAAAAATTATTATTATATATTTAA
3959157 ATTA
63 ATTA
3959161 TATCACATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
67 16 0.28
68 33 0.58
69 8 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (67 bp):
AAAATATTAAAATATAAATATTTATATTATAATTTATATAAAAATTATTATTATATATTTAAATT
AA
Found at i:3959204 original size:24 final size:25
Alignment explanation
Indices: 3959158--3959218 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
3959148 TATATTTAAA
* **
3959158 TTATATCACATTTATATTTTATT-T
1 TTATATCATATTTATATCATATTAT
*
3959182 TTATATTATATTTATATCATATTAT
1 TTATATCATATTTATATCATATTAT
3959207 TT-TATCATATTT
1 TTATATCATATTT
3959219 TAAATAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATATCATATTTATATCATATTAT
Found at i:3974441 original size:21 final size:20
Alignment explanation
Indices: 3974415--3974466 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
3974405 ATAAATATTT
3974415 TTAATATTTTATTAATAAATA
1 TTAATATTTTATTAAT-AATA
*
3974436 TTAATATTATT-TTAATATTA
1 TTAATATT-TTATTAATAATA
*
3974456 TGAATATTTTA
1 TTAATATTTTA
3974467 ATTATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 10 0.37
21 13 0.48
22 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATATTTTATTAATAATA
Found at i:3974442 original size:30 final size:32
Alignment explanation
Indices: 3974393--3974454 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 32
3974383 TTATTTTATA
*
3974393 TTATTATTAAACATAAATA-T-TTTTAATATT
1 TTATTAATAAACATAAATATTATTTTAATATT
* *
3974423 TTATTAATAAATATTAATATTATTTTAATATT
1 TTATTAATAAACATAAATATTATTTTAATATT
3974455 ATGAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 16 0.59
31 1 0.04
32 10 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
TTATTAATAAACATAAATATTATTTTAATATT
Found at i:3974487 original size:26 final size:28
Alignment explanation
Indices: 3974384--3974488 Score: 72
Period size: 26 Copynumber: 4.1 Consensus size: 28
3974374 TAAATATTTT
*
3974384 TATTTT-ATATTATTATTAA-A-CATAAA
1 TATTTTAATATTATT-TTAATATTATAAA
* *
3974410 TATTTT--TAATATTTT-AT-TAATAAA
1 TATTTTAATATTATTTTAATATTATAAA
*
3974434 TA--TTAATATTATTTTAATATTATGAA
1 TATTTTAATATTATTTTAATATTATAAA
3974460 TATTTTAATTATT-TTTTAAT-TTA-AAA
1 TATTTTAA-TATTATTTTAATATTATAAA
3974486 TAT
1 TAT
3974489 ATTATTTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
22 2 0.03
23 1 0.02
24 17 0.27
25 8 0.12
26 18 0.28
27 3 0.05
28 11 0.17
29 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTTTAATATTATTTTAATATTATAAA
Found at i:3974614 original size:15 final size:15
Alignment explanation
Indices: 3974589--3974654 Score: 64
Period size: 15 Copynumber: 4.5 Consensus size: 15
3974579 AATACTTTCA
* *
3974589 ATATAAAATATAATT
1 ATATTAAATATTATT
*
3974604 ATTTTAAATATT-TT
1 ATATTAAATATTATT
*
3974618 ACTATTAAATATTACT
1 A-TATTAAATATTATT
*
3974634 AT-TTTAATATTATT
1 ATATTAAATATTATT
3974648 ATATTAA
1 ATATTAA
3974655 TAATGTAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 15 0.38
15 23 0.57
16 2 0.05
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTAAATATTATT
Found at i:3974637 original size:30 final size:29
Alignment explanation
Indices: 3974589--3974672 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 29
3974579 AATACTTTCA
* *
3974589 ATATAAAATATAATTATTTTAAATATT-TT
1 ATATTAAATATAACTATTTT-AATATTATT
*
3974618 ACTATTAAATATTACTATTTTAATATTATT
1 A-TATTAAATATAACTATTTTAATATTATT
*
3974648 ATATTAATAATGTAA-TATTTTAATA
1 ATATT-A-AATATAACTATTTTAATA
3974673 ATAGTAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 11 0.24
30 30 0.65
31 5 0.11
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (29 bp):
ATATTAAATATAACTATTTTAATATTATT
Found at i:3974644 original size:14 final size:14
Alignment explanation
Indices: 3974616--3974672 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
3974606 TTTAAATATT
*
3974616 TTACTA-TTAAATA
1 TTACTATTTTAATA
3974629 TTACTATTTTAATA
1 TTACTATTTTAATA
* *
3974643 TTATTATATTAATAA
1 TTACTATTTTAAT-A
*
3974658 TGTAATATTTTAATA
1 T-TACTATTTTAATA
3974673 ATAGTAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 6 0.17
14 17 0.47
15 3 0.08
16 10 0.28
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (14 bp):
TTACTATTTTAATA
Found at i:3974696 original size:15 final size:14
Alignment explanation
Indices: 3974625--3974703 Score: 60
Period size: 14 Copynumber: 5.8 Consensus size: 14
3974615 TTTACTATTA
*
3974625 AATATTACTATTTT
1 AATATTAATATTTT
* *
3974639 AATATTATTATATT
1 AATATTAATATTTT
3974653 AATAATGTAATATTTT
1 AAT-AT-TAATATTTT
*
3974669 -A-A-TAATA--GT
1 AATATTAATATTTT
3974678 AATATTAATATTTT
1 AATATTAATATTTT
3974692 AAATATTAATAT
1 -AATATTAATAT
3974704 AAATAATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
9 1 0.02
10 1 0.02
11 6 0.12
12 5 0.10
13 1 0.02
14 16 0.31
15 14 0.27
16 7 0.14
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (14 bp):
AATATTAATATTTT
Found at i:3974708 original size:21 final size:23
Alignment explanation
Indices: 3974661--3974708 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
3974651 TTAATAATGT
*
3974661 AATATTTTAATAATAGTAATATT
1 AATATTTTAATAATAGTAATATA
*
3974684 AATATTTT-A-AATATTAATATA
1 AATATTTTAATAATAGTAATATA
3974705 AATA
1 AATA
3974709 ATAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 1 0.04
23 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
AATATTTTAATAATAGTAATATA
Found at i:3974977 original size:14 final size:14
Alignment explanation
Indices: 3974954--3974999 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
3974944 CAAAAAATAT
3974954 AAATATTTTTCAAA
1 AAATATTTTTCAAA
*
3974968 AAATAATTTTT-ATA
1 AAAT-ATTTTTCAAA
3974982 AAATATTTTTCATAA
1 AAATATTTTTCA-AA
3974997 AAA
1 AAA
3975000 GAAGGAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 6 0.22
14 11 0.41
15 10 0.37
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATTTTTCAAA
Found at i:3975503 original size:14 final size:15
Alignment explanation
Indices: 3975479--3975507 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3975469 AATTTATATC
3975479 AATATAAAAATATAA
1 AATATAAAAATATAA
3975494 AATAT-AAAATATAA
1 AATATAAAAATATAA
3975508 TTTTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATATAAAAATATAA
Found at i:3975820 original size:2 final size:2
Alignment explanation
Indices: 3975815--3975843 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3975805 CACTCGCATT
3975815 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3975844 CGCCTTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3984638 original size:23 final size:24
Alignment explanation
Indices: 3984604--3984658 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
3984594 TTTAATATCT
* *
3984604 AAATATAAAATTACATAAAT-ATA
1 AAATATATAATTAAATAAATAATA
3984627 AAATATATAATTAAATAAATAATA
1 AAATATATAATTAAATAAATAATA
*
3984651 AAAAATAT
1 AAATATAT
3984659 TATATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAATATATAATTAAATAAATAATA
Found at i:3986216 original size:10 final size:9
Alignment explanation
Indices: 3986161--3986219 Score: 59
Period size: 10 Copynumber: 6.4 Consensus size: 9
3986151 ATTATTTAAA
3986161 TAATATTTT
1 TAATATTTT
*
3986170 TATTA-TTT
1 TAATATTTT
*
3986178 TAATA-ATT
1 TAATATTTT
3986186 TAAGTATTTT
1 TAA-TATTTT
3986196 TAATCATTTT
1 TAAT-ATTTT
3986206 TAATATGTTT
1 TAATAT-TTT
3986216 TAAT
1 TAAT
3986220 TTAAAATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 12 0.29
9 9 0.21
10 21 0.50
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TAATATTTT
Found at i:3986619 original size:26 final size:26
Alignment explanation
Indices: 3986565--3986621 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
3986555 ATAAATATAG
*
3986565 TAATAAATAATTTCAATTTATTTTAT
1 TAATAAATAATTTCAATATATTTTAT
* *
3986591 TAATAAATAATTTTAA-ATATTTATGT
1 TAATAAATAATTTCAATATATTT-TAT
3986617 TAATA
1 TAATA
3986622 TTATTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (26 bp):
TAATAAATAATTTCAATATATTTTAT
Found at i:3988201 original size:20 final size:20
Alignment explanation
Indices: 3988160--3988225 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
3988150 ATACATAATT
*
3988160 TTATTTAAAATTATGAATAA
1 TTATTTAAAATTATAAATAA
*
3988180 TTATTTTAAA-TATAAATAAA
1 TTATTTAAAATTATAAAT-AA
*
3988200 TTAATT--AATTATTAAATAA
1 TTATTTAAAATTA-TAAATAA
3988219 TATATTT
1 T-TATTT
3988226 TTATCAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.05
19 11 0.29
20 25 0.66
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TTATTTAAAATTATAAATAA
Found at i:3988574 original size:18 final size:21
Alignment explanation
Indices: 3988551--3988590 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3988541 CCGTGATATT
3988551 AAATTT-AATT-AA-AAATAA
1 AAATTTAAATTCAATAAATAA
3988569 AAATTTAAATTCAATAAATAA
1 AAATTTAAATTCAATAAATAA
3988590 A
1 A
3988591 TATAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 2 0.11
21 7 0.37
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATTTAAATTCAATAAATAA
Found at i:3988963 original size:15 final size:15
Alignment explanation
Indices: 3988943--3988996 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
3988933 GAAATTTTAT
3988943 AATTTTTTGAAAATA
1 AATTTTTTGAAAATA
***
3988958 AATTTTAAAAAAATCA
1 AATTTTTTGAAAAT-A
3988974 TATATTTTTTGAAAATA
1 -A-ATTTTTTGAAAATA
3988991 AATTTT
1 AATTTT
3988997 CAAATTTCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 16 0.53
16 2 0.07
17 2 0.07
18 10 0.33
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
AATTTTTTGAAAATA
Found at i:3989999 original size:14 final size:16
Alignment explanation
Indices: 3989973--3990004 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3989963 AAAAAATATT
3989973 AAAATAAACAA-TTAA
1 AAAATAAACAATTTAA
3989988 AAAATAAA-AATTTAA
1 AAAATAAACAATTTAA
3990003 AA
1 AA
3990005 CTGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 14 0.88
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATAAACAATTTAA
Found at i:3990307 original size:16 final size:17
Alignment explanation
Indices: 3990272--3990309 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3990262 TTTTAATTAT
* *
3990272 ATAAATATAATATTTTA
1 ATAAATATAAAATTTAA
3990289 ATAAAT-TAAAATTTAA
1 ATAAATATAAAATTTAA
3990305 ATAAA
1 ATAAA
3990310 AATTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAATATAAAATTTAA
Found at i:3997069 original size:2 final size:2
Alignment explanation
Indices: 3997062--3997092 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3997052 GTTCTTTAAT
3997062 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3997093 CAGAAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3997277 original size:27 final size:28
Alignment explanation
Indices: 3997229--3997281 Score: 65
Period size: 26 Copynumber: 1.9 Consensus size: 28
3997219 TTGTAATGTG
* *
3997229 TTTTATATTTTATGTTTTTAAAATTTTTA
1 TTTTATATTTTATATTTAT-AAATTTTTA
3997258 TTTTAT-TTTTA-ATTTATAAATTTT
1 TTTTATATTTTATATTTATAAATTTT
3997282 GAAAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 4 0.18
28 5 0.23
29 6 0.27
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (28 bp):
TTTTATATTTTATATTTATAAATTTTTA
Found at i:3998506 original size:21 final size:20
Alignment explanation
Indices: 3998469--3998509 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3998459 ATTTGATTCG
*
3998469 ATTTTTTAAAATTAATTTTT
1 ATTTTTAAAAATTAATTTTT
*
3998489 ATTTTTAAAAATTAAATTTT
1 ATTTTTAAAAATTAATTTTT
3998509 A
1 A
3998510 AATTAGATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAAATTAATTTTT
Found at i:3998628 original size:8 final size:8
Alignment explanation
Indices: 3998617--3998653 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
3998607 AATTTTTTAA
3998617 TTATATAT
1 TTATATAT
*
3998625 TTATATAA
1 TTATATAT
3998633 TTATATA-
1 TTATATAT
3998640 TTATATAT
1 TTATATAT
3998648 TTATAT
1 TTATAT
3998654 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATATAT
Found at i:3998678 original size:29 final size:29
Alignment explanation
Indices: 3998600--3998678 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
3998590 ATATTTATAT
3998600 AAAAATTA-ATTTT-TTAATTATATATTTA
1 AAAAATTATATTTTATTAATT-TATATTTA
* * *
3998628 TATAATTATATATTA-TATATTTATATTTA
1 AAAAATTATATTTTATTA-ATTTATATTTA
*
3998657 AAAAATAATATTTTATTAATTT
1 AAAAATTATATTTTATTAATTT
3998679 CGAATCAGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 6 0.15
29 29 0.73
30 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
AAAAATTATATTTTATTAATTTATATTTA
Found at i:3999121 original size:19 final size:19
Alignment explanation
Indices: 3999099--3999139 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3999089 TTATTTAAAT
*
3999099 ATAATAAAAATAAATATGA
1 ATAATAAAAATAAATACGA
* *
3999118 ATAATATAAATATATACGA
1 ATAATAAAAATAAATACGA
3999137 ATA
1 ATA
3999140 GACACGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATAAATACGA
Found at i:3999643 original size:9 final size:9
Alignment explanation
Indices: 3999588--3999645 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
3999578 TTTATATATT
3999588 TATATTAAA
1 TATATTAAA
* *
3999597 TTAAAATAAA
1 -TATATTAAA
**
3999607 TATAAAAAA
1 TATATTAAA
*
3999616 TATGTTAAA
1 TATATTAAA
*
3999625 CATATTAAA
1 TATATTAAA
3999634 TATATTAAA
1 TATATTAAA
3999643 TAT
1 TAT
3999646 GTACTCGTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
9 31 0.82
10 7 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (9 bp):
TATATTAAA
Found at i:4000821 original size:2 final size:2
Alignment explanation
Indices: 4000814--4000840 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4000804 CTTCATTAAA
4000814 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
4000841 ATGCTTACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:4007405 original size:19 final size:20
Alignment explanation
Indices: 4007369--4007406 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
4007359 AAGATTATTC
* *
4007369 TTTATTTTTTTAATTTTTAA
1 TTTATTTTTTAAAATTTTAA
4007389 TTTA-TTTTTAAAATTTTA
1 TTTATTTTTTAAAATTTTA
4007407 TCCTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTTTTAAAATTTTAA
Found at i:4020935 original size:22 final size:22
Alignment explanation
Indices: 4020910--4020952 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4020900 AATAATAATA
*
4020910 ATTATAACTATTATTAAAAAAT
1 ATTATAACTATGATTAAAAAAT
*
4020932 ATTATAATTATGATTAAAAAA
1 ATTATAACTATGATTAAAAAA
4020953 ATTTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTATAACTATGATTAAAAAAT
Found at i:4032679 original size:25 final size:25
Alignment explanation
Indices: 4032625--4032676 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
4032615 AATAATAATT
4032625 ATTATTATAATTATAATTGAAAAAA
1 ATTATTATAATTATAATTGAAAAAA
* *
4032650 ATTATTGTAATTGTAATT-AAAAAA
1 ATTATTATAATTATAATTGAAAAAA
4032674 ATT
1 ATT
4032677 TATAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (25 bp):
ATTATTATAATTATAATTGAAAAAA
Found at i:4034820 original size:2 final size:2
Alignment explanation
Indices: 4034813--4034840 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4034803 CGCATCAAAT
4034813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4034841 GTGATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4036155 original size:58 final size:58
Alignment explanation
Indices: 4036087--4036487 Score: 305
Period size: 58 Copynumber: 6.8 Consensus size: 58
4036077 CTAAAATTTT
* **
4036087 TTTTTG-AGAAAAAGTTGAAAGTATCAATTTTCCTTAAAACCAAAATTTTGAAAAGTA
1 TTTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTTGAAAAGTA
* * * **
4036144 TTTTTGAA-GAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAA
1 TTTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTT---TGA-AAAGTA
* * * *
4036206 TATTTTGAA-AAAAAATTGAAAGTATCAATTTTCCTTAAAAATGAAATTTCGAAAAGTA
1 T-TTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTTGAAAAGTA
* * ** *
4036264 TTTTTG-AGGAAAAGTTGAAAATATCAATTTTTCTCGAAAATAAAAATTTCAATTCTGAAAAATA
1 TTTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAA--T---TT-TGAAAAGTA
* * * ** **
4036328 -TCTTG-AGGAAAAGTTGAAAGTATTAATTTT-TTGTAAAAATAAAATTTCAAAAAGCG
1 TTTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCT-TAAAAATAAAATTTTGAAAAGTA
* * * * * **
4036384 TTTTTTAAGGAAAAGTTGAAAGTATTAGTTTTCTTTAAAAATAAAATTTTCAAAAAGCG
1 TTTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTT-GAAAAGTA
* * *
4036443 GTTTTGAA-GAAAAGTTGAAAGTATCAATTTCCCTTGAAAATAAAA
1 TTTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAA
4036488 ATAAAAAAAA
Statistics
Matches: 276, Mismatches: 48, Indels: 39
0.76 0.13 0.11
Matches are distributed among these distances:
56 5 0.02
57 71 0.26
58 86 0.31
59 17 0.06
60 2 0.01
61 2 0.01
62 16 0.06
63 70 0.25
64 7 0.03
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
TTTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTTGAAAAGTA
Found at i:4036214 original size:63 final size:62
Alignment explanation
Indices: 4036145--4036602 Score: 244
Period size: 63 Copynumber: 7.5 Consensus size: 62
4036135 TGAAAAGTAT
4036145 TTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAATA
1 TTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTCAAAAAT-AAAATTTCAATTATAAAAAATA
* * * * * * **
4036208 TTTTGAAAAAAAATTGAAAGTATCAATTTTCCTTAAAAATGAAATTTC---GA-AAAGTAT-
1 TTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAATTTCAATTATAAAAAATA
* * * * *
4036265 TTTTGAGGAAAAGTTGAAAATATCAATTTTTCTCGAAAATAAAAATTTCAATTCTGAAAAATA
1 TTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTCAAAAAT-AAAATTTCAATTATAAAAAATA
* * * * ***
4036328 TCTTGAGGAAAAGTTGAAAGTATTAATTTTT-TGTAAAAATAAAATTTC-A--A-AAAGCGT-
1 TTTTGAAGAAAAGTTGAAAGTATCAATTTTTCT-CAAAAATAAAATTTCAATTATAAAAAATA
* * * * * ****
4036385 TTTTTAAGGAAAAGTTGAAAGTAT-TAGTTTTCTTTAAAAATAAAATTT---TCA-AAAAGCGG
1 TTTTGAA-GAAAAGTTGAAAGTATCAATTTTTC-TCAAAAATAAAATTTCAATTATAAAAAATA
** ** ***
4036444 TTTTGAAGAAAAGTTGAAAGTATCAATTTCCCTTGAAAATAAAAATAAAAAAAATTCA-AAAAAA
1 TTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTCAAAAAT-AAAAT---TTCAATT-ATAAAAAA
*
4036508 AA
61 TA
*
4036510 TCTTTG-AGTAAAAGTTGAAAATATC-ATTTTTCTTTC-AAAATAAAATCTTCAA--A-AAAGGA
1 T-TTTGAAG-AAAAGTTGAAAGTATCAATTTTTC--TCAAAAATAAAAT-TTCAATTATAAA--A
4036569 AATA
59 AATA
4036573 TTTT-AAGAAAAAGTTGAAAGTATCAATTTT
1 TTTTGAAG-AAAAGTTGAAAGTATCAATTTT
4036603 CTTTGACTTA
Statistics
Matches: 301, Mismatches: 64, Indels: 60
0.71 0.15 0.14
Matches are distributed among these distances:
57 42 0.14
58 72 0.24
59 17 0.06
61 5 0.02
62 40 0.13
63 79 0.26
64 2 0.01
65 1 0.00
66 18 0.06
67 24 0.08
68 1 0.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (62 bp):
TTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAATTTCAATTATAAAAAATA
Found at i:4036225 original size:120 final size:120
Alignment explanation
Indices: 4036088--4036436 Score: 450
Period size: 120 Copynumber: 2.9 Consensus size: 120
4036078 TAAAATTTTT
** *
4036088 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAACCAAAATTTTGAAAAGTATTTTTGAAG
1 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCGAAAAGTATTTTTGAAG
4036153 AAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAATA
66 AAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAATA
* * * *
4036208 TTTTGAAAAAAAATTGAAAGTATCAATTTTCCTTAAAAATGAAATTTCGAAAAGTATTTTTGAGG
1 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCGAAAAGTATTTTTGAAG
* * * *
4036273 AAAAGTTGAAAATATCAATTTTTCTCGAAAATAAAAATTTCAATTCTGAAAAATA
66 AAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAATA
* * * * * ** *
4036328 TCTTGAGGAAAAGTTGAAAGTATTAATTTT-TTGTAAAAATAAAATTTCAAAAAGCGTTTTTTAA
1 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCT-TAAAAATAAAATTTCGAAAAGTATTTTTGAA
* * * *
4036392 GGAAAAGTTGAAAGTAT-TAGTTTTCTTTAAAAATAAAATTTTCAA
65 -GAAAAGTTGAAAGTATCAATTTTTC-TCAAAAATAAAAATTTCAA
4036437 AAAGCGGTTT
Statistics
Matches: 197, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
119 1 0.01
120 165 0.84
121 31 0.16
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (120 bp):
TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCGAAAAGTATTTTTGAAG
AAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAATA
Found at i:4036695 original size:14 final size:15
Alignment explanation
Indices: 4036666--4036696 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4036656 TTTAAAAATG
4036666 AAATTTTTAAGAAAA
1 AAATTTTTAAGAAAA
*
4036681 AAATTTTTGAGAAAA
1 AAATTTTTAAGAAAA
4036696 A
1 A
4036697 GTTGAAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (15 bp):
AAATTTTTAAGAAAA
Found at i:4039974 original size:121 final size:121
Alignment explanation
Indices: 4039838--4040345 Score: 487
Period size: 121 Copynumber: 4.1 Consensus size: 121
4039828 TCTAAAAAAC
*
4039838 TTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAATTATAAAAAAAT
1 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAATTAT-AAAAAAT
* * *
4039903 ATTTTGAGAAAAAATTGAAAGTATCAATTTTCCTTAAAAACAAAATTTTGAAAAGCA
65 ATTTTGAAAAAAAATTAAAAGTATCAATTTTCCTTAAAAACAAAATTTCGAAAAGCA
* * * *
4039960 TTTTTT-AGGAAAAGTTAAAAATATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAATA
1 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAATTATAAAAAATA
**
4040024 TTTTGAAAAAAAATTAAAAGTATCAATTTTCCTTAAAAATGAAATTTCGAAAAGCA
66 TTTTGAAAAAAAATTAAAAGTATCAATTTTCCTTAAAAACAAAATTTCGAAAAGCA
***
4040080 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTC-A--A-AAAGCGT-
1 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAATTATAAAAAATA
* * * * *
4040140 TTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTGAGAATAAAAATTAAAAAAAAATTTCAAAAA
66 TTTTGAAAAAAAATTAAAAGTATCAA-TTTTCCT-----T----A--AAAACAAAATTTC-GAAA
**
4040205 AAAA
118 AGCA
* * * * * *
4040209 TATCTTTGAGGAAAAGTTGAAAATATCAATTTTCCTTCAAAATAAAATCTTCAA--AAAAGAAAA
1 T-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAATTATAA-AAAA
* * * * * *
4040272 TATTTT-AAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAATA-AAATTTTCAAAAAAGGA
64 TATTTTGAA-AAAAAATTAAAAGTATCAATTTTCCTTAAAA-ACAAAATTTC-GAAAAGCA
4040331 TTTTTTGAGGAAAAG
1 TTTTTTGAGGAAAAG
4040346 CTTAAATTTT
Statistics
Matches: 324, Mismatches: 41, Indels: 43
0.79 0.10 0.11
Matches are distributed among these distances:
116 24 0.07
117 10 0.03
118 1 0.00
120 66 0.20
121 98 0.30
122 25 0.08
123 1 0.00
124 1 0.00
126 1 0.00
128 12 0.04
129 6 0.02
130 45 0.14
131 2 0.01
132 2 0.01
133 9 0.03
134 21 0.06
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.35
Consensus pattern (121 bp):
TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAATTATAAAAAATA
TTTTGAAAAAAAATTAAAAGTATCAATTTTCCTTAAAAACAAAATTTCGAAAAGCA
Found at i:4040172 original size:58 final size:58
Alignment explanation
Indices: 4039839--4040183 Score: 320
Period size: 58 Copynumber: 5.8 Consensus size: 58
4039829 CTAAAAAACT
**
4039839 TTTTTG-AGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAATTATAAAAAAA
1 TTTTTGAAGAAAAA-TTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTC----A-AAAAGCA
* * *
4039902 TATTTTG-AGAAAAAATTGAAAGTATCAATTTTCCTTAAAAACAAAATTTT-GAAAAGCA
1 T-TTTTGAAG-AAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAGCA
* * * * * * * **
4039960 TTTTTTAGGAAAAGTTAAAAATATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAA
1 TTTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTC-A--A-AAAGCA
* * * * *
4040022 TATTTTGAAAAAAAATTAAAAGTATCAATTTTCCTTAAAAATGAAA-TTTCGAAAAGCA
1 T-TTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAGCA
* * *
4040080 TTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAGCG
1 -TTTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAGCA
* *
4040139 TTTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTGAGAATAAAA
1 TTTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAA
4040184 ATTAAAAAAA
Statistics
Matches: 231, Mismatches: 40, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
57 37 0.16
58 90 0.39
59 12 0.05
61 1 0.00
62 9 0.04
63 37 0.16
64 40 0.17
65 5 0.02
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (58 bp):
TTTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAGCA
Found at i:4040206 original size:71 final size:72
Alignment explanation
Indices: 4040114--4040255 Score: 157
Period size: 72 Copynumber: 2.0 Consensus size: 72
4040104 TCAATTTTTC
** * * * *
4040114 TTAAAAATAAAATTTTCAAAAAGCGT-T-TTTGAAGAAAAATTGAAAGTATCAATTTTTCTTGAG
1 TTAAAAATAAAATTTTCAAAAA-AATATCTTTGAAGAAAAATTGAAAATATCAATTTTCCTTCAA
4040177 AATAAAAA
65 AATAAAAA
* *
4040185 TTAAAAA-AAAA-TTTCAAAAAAAAATATCTTTGAGGAAAAGTTGAAAATATCAATTTTCCTTCA
1 TTAAAAATAAAATTTTC--AAAAAAATATCTTTGAAGAAAAATTGAAAATATCAATTTTCCTTCA
4040248 AAATAAAA
64 AAATAAAA
4040256 TCTTCAAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
69 4 0.07
70 5 0.08
71 13 0.22
72 37 0.63
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (72 bp):
TTAAAAATAAAATTTTCAAAAAAATATCTTTGAAGAAAAATTGAAAATATCAATTTTCCTTCAAA
ATAAAAA
Found at i:4040290 original size:62 final size:61
Alignment explanation
Indices: 4040185--4040328 Score: 195
Period size: 62 Copynumber: 2.4 Consensus size: 61
4040175 AGAATAAAAA
* * *
4040185 TTAAAAAAAAATTTC-AAAAA-AAAATATCTTTGAGGAAAAGTTGAAAATATCAATTTTCC
1 TTAAAATAAAATTTCAAAAAAGAAAATATCTTTAAGAAAAAGTTGAAAATATCAATTTTCC
* *
4040244 TTCAAAATAAAATCTTCAAAAAAGAAAATAT-TTTAAGAAAAAGTTGAAAGTATCAATTTTTC
1 TT-AAAATAAAAT-TTCAAAAAAGAAAATATCTTTAAGAAAAAGTTGAAAATATCAATTTTCC
4040306 TTAAAATAAAATTTTCAAAAAAG
1 TTAAAATAAAA-TTTCAAAAAAG
4040329 GATTTTTTGA
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
59 2 0.03
60 9 0.12
61 22 0.29
62 35 0.47
63 7 0.09
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (61 bp):
TTAAAATAAAATTTCAAAAAAGAAAATATCTTTAAGAAAAAGTTGAAAATATCAATTTTCC
Found at i:4040339 original size:251 final size:244
Alignment explanation
Indices: 4039966--4040431 Score: 572
Period size: 251 Copynumber: 1.9 Consensus size: 244
4039956 AGCATTTTTT
* *
4039966 AGGAAAAGTTAAAAATATCAATTTTTCTCAAAAATAAAAATTTCAATTATAAAAAATATTTTGAA
1 AGGAAAAGTTAAAAATATCAATTTTCCTCAAAAATAAAAATTTCAA-TAAAAAAAATATTTTGAA
* *
4040031 AAAAAATTAAAAGTATCAATTTTCCTTAAAAATGAAATTTCGAAAAGCATTTTTTGAGGAAAAG-
65 AAAAAATTAAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAGCATTTTTTGAGGAAAAGC
* *
4040095 TTGAAAGTATCAATTTTTCTTAAAAAT-AAAATTTT-CAAAAAGCGTTTTTGAAGAAAAA-TTGA
130 TT--AA--AT---TTTCT-TTAAAAATGAAAATTTTACAAAAA-CATTTTTG-AGAAAAAGTTGA
* *
4040157 AAGTATCAATTTTTCTTGAGAATAAAAATTAAAAAAAAATTTCAAAAAAAAATATCTTTG
185 AAGTATCAATTTTTCTTAAAAATAAAAATTAAAAAAAAATTTCAAAAAAAAATATCTTTG
*
4040217 AGGAAAAGTTGAAAATATCAATTTTCCTTC-AAAAT-AAAATCTTCAA-AAAAGAAAATATTTT-
1 AGGAAAAGTTAAAAATATCAATTTTCC-TCAAAAATAAAAAT-TTCAATAAAA-AAAATATTTTG
* * * *
4040278 AAGAAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAAATTTTCAAAAAAGGATTTTTTGAGGA
63 AA-AAAAAATTAAAAGTATCAATTTTCCTTAAAAATAAAA-TTTC-AAAAAGCATTTTTTGAGGA
* *
4040342 AAAGCTTAAATTTTCTTTAAAAATGAAATTTTTAACAAAAATATTTTTGAGAAAAAGTTGAAAGT
125 AAAGCTTAAATTTTCTTTAAAAATGAAAATTTT-ACAAAAACATTTTTGAGAAAAAGTTGAAAGT
4040407 ATCAATTTTTCTTAAAAATAAAAAT
189 ATCAATTTTTCTTAAAAATAAAAAT
4040432 GTCAAAATGC
Statistics
Matches: 189, Mismatches: 15, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
244 8 0.04
245 18 0.10
246 37 0.20
247 6 0.03
248 2 0.01
249 13 0.07
250 45 0.24
251 56 0.30
252 4 0.02
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (244 bp):
AGGAAAAGTTAAAAATATCAATTTTCCTCAAAAATAAAAATTTCAATAAAAAAAATATTTTGAAA
AAAAATTAAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAGCATTTTTTGAGGAAAAGCT
TAAATTTTCTTTAAAAATGAAAATTTTACAAAAACATTTTTGAGAAAAAGTTGAAAGTATCAATT
TTTCTTAAAAATAAAAATTAAAAAAAAATTTCAAAAAAAAATATCTTTG
Found at i:4059499 original size:21 final size:22
Alignment explanation
Indices: 4059460--4059500 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
4059450 AAAAATCTCC
4059460 AAATTTATTATTTTGTTTAAAT
1 AAATTTATTATTTTGTTTAAAT
4059482 AAATTT-TTATATTT-TTTAA
1 AAATTTATTAT-TTTGTTTAA
4059501 CATCTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
AAATTTATTATTTTGTTTAAAT
Found at i:4059553 original size:29 final size:31
Alignment explanation
Indices: 4059495--4059588 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 31
4059485 TTTTTATATT
* * *
4059495 TTTTAACATCTAAATAAGTTCTT-GATTTTTA
1 TTTT-ACATCTAAATAAGTTTTTAAAATTTTA
4059526 TTTTACATC-AAATAA-TTTTTAAAATTTTA
1 TTTTACATCTAAATAAGTTTTTAAAATTTTA
* * * *
4059555 ATTTATATCTAAATAAGTTTTTAATATTTAA
1 TTTTACATCTAAATAAGTTTTTAAAATTTTA
4059586 TTT
1 TTT
4059589 ATATATAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.08
29 19 0.37
30 11 0.21
31 18 0.35
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTTACATCTAAATAAGTTTTTAAAATTTTA
Found at i:4059585 original size:30 final size:30
Alignment explanation
Indices: 4059477--4059598 Score: 110
Period size: 30 Copynumber: 4.2 Consensus size: 30
4059467 TTATTTTGTT
*
4059477 TAAATAAATTTTT-ATATTT--TTTAACATC
1 TAAATAAGTTTTTAATATTTAATTT-ACATC
* * * *
4059505 TAAATAAGTTCTTGATTTTTATTTTACATC
1 TAAATAAGTTTTTAATATTTAATTTACATC
* *
4059535 -AAATAA-TTTTTAAAATTTTAATTTATATC
1 TAAATAAGTTTTTAATA-TTTAATTTACATC
* *
4059564 TAAATAAGTTTTTAATATTTAATTTATATA
1 TAAATAAGTTTTTAATATTTAATTTACATC
4059594 TAAAT
1 TAAAT
4059599 TTATTTTAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
28 16 0.21
29 22 0.29
30 28 0.36
31 11 0.14
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (30 bp):
TAAATAAGTTTTTAATATTTAATTTACATC
Found at i:4060573 original size:14 final size:15
Alignment explanation
Indices: 4060537--4060576 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
4060527 TTGTTTTATG
*
4060537 TAATTTGTATATAAT
1 TAATTTTTATATAAT
*
4060552 TCATTTTTATAT-AT
1 TAATTTTTATATAAT
4060566 TAATTTTTATA
1 TAATTTTTATA
4060577 ATTTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (15 bp):
TAATTTTTATATAAT
Found at i:4061186 original size:28 final size:27
Alignment explanation
Indices: 4061132--4061208 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
4061122 TAAATTATAG
*
4061132 TAAAA-TTTTTAATGTAACATTTGAAATT
1 TAAAATTTTTTAA-GTAATATTTGAAA-T
4061160 TAAAATTTTTTAACGTAATATTT-AAAT
1 TAAAATTTTTTAA-GTAATATTTGAAAT
* *
4061187 TATAAATTTATTAATTAATATT
1 TA-AAATTTTTTAAGTAATATT
4061209 ATCTTCTCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
27 10 0.23
28 18 0.42
29 15 0.35
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (27 bp):
TAAAATTTTTTAAGTAATATTTGAAAT
Found at i:4061284 original size:21 final size:19
Alignment explanation
Indices: 4061236--4061274 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
4061226 AATTAATTTC
4061236 AAATAATAATATATAATTA
1 AAATAATAATATATAATTA
4061255 AAA-AATAATAT-TAATTA
1 AAATAATAATATATAATTA
4061272 AAA
1 AAA
4061275 GATTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 8 0.40
19 3 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATAATATATAATTA
Found at i:4061705 original size:4 final size:4
Alignment explanation
Indices: 4061698--4061728 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
4061688 TATATATATA
*
4061698 TATT TATT TATT TATT TTTT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
4061729 ATGCCTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:4063081 original size:2 final size:2
Alignment explanation
Indices: 4063063--4063103 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
4063053 GGACATTTCA
* *
4063063 AT AT AT AC AT A- AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4063104 TTTGTATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4066930 original size:14 final size:16
Alignment explanation
Indices: 4066908--4066940 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
4066898 CTTTTTTTGT
4066908 AAATATTAAATTT-TA
1 AAATATTAAATTTATA
4066923 AAAT-TTAAATTTATA
1 AAATATTAAATTTATA
4066938 AAA
1 AAA
4066941 AATAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTAAATTTATA
Found at i:4070623 original size:16 final size:15
Alignment explanation
Indices: 4070604--4070637 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4070594 TTTTTTCATT
4070604 TTTCTCATTTTTTTTC
1 TTTCT-ATTTTTTTTC
*
4070620 TTTCTTTTTTTTTTC
1 TTTCTATTTTTTTTC
4070635 TTT
1 TTT
4070638 TTTTTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTCTATTTTTTTTC
Found at i:4070627 original size:11 final size:11
Alignment explanation
Indices: 4070612--4070657 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
4070602 TTTTTCTCAT
4070612 TTTTTTTCTTTC
1 TTTTTTT-TTTC
4070624 TTTTTTTTTTC
1 TTTTTTTTTTC
4070635 TTTTTTTTTTC
1 TTTTTTTTTTC
* *
4070646 ATCTTTTTTTC
1 TTTTTTTTTTC
4070657 T
1 T
4070658 CATTTTTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 24 0.77
12 7 0.23
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:4070629 original size:15 final size:14
Alignment explanation
Indices: 4070611--4070655 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
4070601 ATTTTTCTCA
4070611 TTTTTTTTCTTTCTT
1 TTTTTTTTCTTT-TT
4070626 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTT
**
4070640 TTTTTCATCTTTTT
1 TTTTTTTTCTTTTT
4070654 TT
1 TT
4070656 CTCATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTTTCTTTTT
Found at i:4070650 original size:14 final size:13
Alignment explanation
Indices: 4070602--4070655 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 13
4070592 TATTTTTTCA
4070602 TTTTTCTCATTTTT
1 TTTTTCTC-TTTTT
4070616 TTTCTT-TC-TTTT
1 TTT-TTCTCTTTTT
4070628 TTTTT-TCTTTTT
1 TTTTTCTCTTTTT
4070640 TTTTTCATCTTTTT
1 TTTTTC-TCTTTTT
4070654 TT
1 TT
4070656 CTCATTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.11
12 16 0.44
14 14 0.39
15 2 0.06
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCTCTTTTT
Found at i:4070650 original size:25 final size:27
Alignment explanation
Indices: 4070602--4070655 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
4070592 TATTTTTTCA
*
4070602 TTTTTCTCATTTTTTTTCTTTCTTTTT
1 TTTTTCTCATTTTTTTTCTATCTTTTT
*
4070629 TTTTTCT-TTTTTTTTTC-ATCTTTTT
1 TTTTTCTCATTTTTTTTCTATCTTTTT
4070654 TT
1 TT
4070656 CTCATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.36
26 9 0.36
27 7 0.28
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (27 bp):
TTTTTCTCATTTTTTTTCTATCTTTTT
Found at i:4070663 original size:25 final size:25
Alignment explanation
Indices: 4070602--4070664 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
4070592 TATTTTTTCA
4070602 TTTTTCTCATTTTTTTTCTTTCTTT
1 TTTTTCTCATTTTTTTTCTTTCTTT
*
4070627 TTTTTTTC--TTTTTTT-TTTCATCTT
1 TTTTTCTCATTTTTTTTCTTTC-T-TT
4070651 TTTTTCTCATTTTT
1 TTTTTCTCATTTTT
4070665 CATCCATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 9 0.28
25 7 0.22
26 4 0.12
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTCTCATTTTTTTTCTTTCTTT
Found at i:4075340 original size:27 final size:26
Alignment explanation
Indices: 4075250--4075340 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 26
4075240 TTTGTGTAGA
*
4075250 AAAAATTAATACTTTCAACTTTTTTTC
1 AAAAATT-ATACTTTCAACTTTTTTCC
* * *
4075277 AAAAA-TATTCTTCTGAAACTTTAATTTCG
1 AAAAATTATACTT-T-CAACTTT--TTTCC
4075306 AGGAAAATTGATACTTTCAACTTTTTTCC
1 A--AAAATT-ATACTTTCAACTTTTTTCC
4075335 AAAAAT
1 AAAAAT
4075341 ATTTTTTGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
25 5 0.10
26 2 0.04
27 16 0.33
29 9 0.18
31 10 0.20
32 2 0.04
33 5 0.10
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.42
Consensus pattern (26 bp):
AAAAATTATACTTTCAACTTTTTTCC
Found at i:4075374 original size:59 final size:58
Alignment explanation
Indices: 4075251--4075596 Score: 427
Period size: 59 Copynumber: 5.9 Consensus size: 58
4075241 TTGTGTAGAA
* * * * * *
4075251 AAAATTAATACTTTCAACTTTTTTTCAAAAATATTCTTCTGAAACTTT-AATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATT-TTTTGAAAATTTGATTTTCGAAG
4075309 AAAATTGATACTTTCAACTTTTT-TCCAAAAATATTTTTTGAAAAATTTGATTTTCGAAG
1 AAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTTG-AAAATTTGATTTTCGAAG
* * *
4075368 AAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTTG-AAATTT-ATTTT-TAAG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTGATTTTCGAAG
*
4075423 AAAAATTGATACTTTCAAC-TTTTCTCCAAAAATATTTTTTGAAAACTTTGATTTTCGAAA
1 -AAAATTGATACTTTCAACTTTTTCT-CAAAAATATTTTTTGAAAA-TTTGATTTTCGAAG
* * **
4075483 AAAATTGATACTTTCAACTTTTTCTCAAAAACTTTTTTTTTG-AAATTTTATTTTAAAAG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAA--TATTTTTTGAAAATTTGATTTTCGAAG
*
4075542 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTGATTTTC
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAA-TTTGATTTTC
4075597 AAGTTTCAAC
Statistics
Matches: 252, Mismatches: 21, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
55 8 0.03
56 37 0.15
57 22 0.09
58 44 0.17
59 121 0.48
60 12 0.05
61 8 0.03
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAAATTTGATTTTCGAAG
Found at i:4075547 original size:174 final size:169
Alignment explanation
Indices: 4075250--4075880 Score: 665
Period size: 174 Copynumber: 3.7 Consensus size: 169
4075240 TTTGTGTAGA
* * * * * *
4075250 AAAAATTAATACTTTCAACTTTTTTTCAAAAA-TATTCTTCTGAAACTTTAATTTCG-AGGAAAA
1 AAAAATTGATACTTTCAACTTTTCTCCAAAAACT-TT-TTTTGAAA-TTT-ATTTTGAAGAAAAA
* * *
4075313 TTGATACTTTCAACTTTTT-TCCAAAAA-TATTTTTTGAAAAATTTGATTTTCGAAGAAAATTGA
62 TTGATACTTTCAACTTTTTCT-CAAAAATTTTTTTTTG--AAATTTTATTTT-AAAGAAAATTGA
*
4075376 TACTTTCAACTTTTCCTCAAAAATTTTTTTTGAAATTTATTTTTAAG
123 TACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTATTTTTAAG
4075423 AAAAATTGATACTTTCAACTTTTCTCCAAAAA-TATTTTTTGAAAACTTTGATTTTCGAA-AAAA
1 AAAAATTGATACTTTCAACTTTTCTCCAAAAACT-TTTTTTG-AAA-TTT-ATTTT-GAAGAAAA
4075486 ATTGATACTTTCAACTTTTTCTCAAAAACTTTTTTTTTGAAATTTTATTTTAAAAGAAAATTGAT
61 ATTGATACTTTCAACTTTTTCTCAAAAA-TTTTTTTTTGAAATTTTATTTT-AAAGAAAATTGAT
*
4075551 ACTTTCAACTTTTCCTCAAAAATATTTTTTGAAA---A-CTTT--G
124 ACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTATTTTTAAG
** * * * *
4075591 --ATTTTCA-AGTTTCAACTTTTCTTCAAAAACCTTTTTTTGAAATTTATTTTTAAGAAAAATTG
1 AAAAATTGATACTTTCAACTTTTCTCCAAAAA-CTTTTTTTGAAATTTATTTTGAAGAAAAATTG
** *
4075653 ATACTTTCAAC-TTTTCTTCAAAACCTTTTTTTTGAAA-TTTATTTTTAAGAAAAATTGATACTT
65 ATACTTTCAACTTTTTC-TCAAAAATTTTTTTTTGAAATTTTATTTTAAAG-AAAATTGATACTT
4075716 TCAACTTTT-CTCCAAAAATATTTTTTGAAAACTTTGATTTTTAAG
128 TCAACTTTTCCT-CAAAAATATTTTTTG-AAA-TTT-ATTTTTAAG
* *
4075761 GAAAATTGATACTTTCAACTTTTC-CTCAAAAACCTTTTTTTGAAATTTTATTTTTAAGAAAAAT
1 AAAAATTGATACTTTCAACTTTTCTC-CAAAAA-CTTTTTTTGAAA-TTTATTTTGAAGAAAAAT
* *
4075825 TGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTG-GATTTTA-TTTAAAGAAAAT
63 TGATACTTTCAACTTTTTCTCAAAAAT-TTTTTTTTGAAATTTTATTTTAAAGAAAAT
4075881 AAAATAATAA
Statistics
Matches: 396, Mismatches: 33, Indels: 58
0.81 0.07 0.12
Matches are distributed among these distances:
160 5 0.01
161 45 0.11
162 22 0.06
163 30 0.08
164 3 0.01
165 23 0.06
166 11 0.03
167 2 0.01
168 4 0.01
170 4 0.01
171 1 0.00
172 8 0.02
173 81 0.20
174 129 0.33
175 20 0.05
176 8 0.02
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (169 bp):
AAAAATTGATACTTTCAACTTTTCTCCAAAAACTTTTTTTGAAATTTATTTTGAAGAAAAATTGA
TACTTTCAACTTTTTCTCAAAAATTTTTTTTTGAAATTTTATTTTAAAGAAAATTGATACTTTCA
ACTTTTCCTCAAAAATATTTTTTGAAATTTATTTTTAAG
Found at i:4075710 original size:279 final size:278
Alignment explanation
Indices: 4075320--4075858 Score: 860
Period size: 279 Copynumber: 1.9 Consensus size: 278
4075310 AAATTGATAC
4075320 TTTCAACTTTTTTCCAAAAATATTTTTTGAAAAATTTGATTTTCGAAGAAAATTGATACTTTCAA
1 TTTCAACTTTTTTCCAAAAATATTTTTTG-AAAATTTGATTTTCGAAGAAAATTGATACTTTCAA
4075385 CTTTTCCTCAAAAATTTTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCTCC
65 CTTTTCCTCAAAAATTTTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCTCC
*
4075450 AAAAATATTTTTTGAAAACTTTGATTTTCGAA-AAAAATTGATACTTTCAACTTTTTCTCAAAAA
130 AAAAATATTTTTTGAAAACTTTGATTTT-GAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA
*
4075514 CTTTTTTTTTGAAATTTTATTTTAAA-AGAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATT
194 C-CTTTTTTTGAAATTTTATTTTAAAGA-AAAATTGATACTTTCAACTTTTTCC-CAAAAATATT
4075577 TTTTGAAAACTTTGATTTTCAAG
256 TTTTGAAAACTTTGATTTTCAAG
*
4075600 TTTCAACTTTTCTT-CAAAAACCT-TTTTTTG-AAATTT-ATTTT-TAAGAAAAATTGATACTTT
1 TTTCAACTTTT-TTCCAAAAA--TATTTTTTGAAAATTTGATTTTCGAAG-AAAATTGATACTTT
* *
4075660 CAACTTTTCTTCAAAACCTTTTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTT
62 CAACTTTTCCTCAAAA-ATTTTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTT
* *
4075725 CTCCAAAAATATTTTTTGAAAACTTTGATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCAA
126 CTCCAAAAATATTTTTTGAAAACTTTGATTTTGAAGAAAAATTGATACTTTCAACTTTTCCTCAA
*
4075790 AAACCTTTTTTTGAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATT
191 AAACCTTTTTTTGAAATTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATT
4075855 TTTT
256 TTTT
4075859 TTGGATTTTA
Statistics
Matches: 243, Mismatches: 8, Indels: 18
0.90 0.03 0.07
Matches are distributed among these distances:
277 3 0.01
278 90 0.37
279 123 0.51
280 17 0.07
281 9 0.04
282 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (278 bp):
TTTCAACTTTTTTCCAAAAATATTTTTTGAAAATTTGATTTTCGAAGAAAATTGATACTTTCAAC
TTTTCCTCAAAAATTTTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCTCCA
AAAATATTTTTTGAAAACTTTGATTTTGAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAACC
TTTTTTTGAAATTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTG
AAAACTTTGATTTTCAAG
Found at i:4075740 original size:58 final size:57
Alignment explanation
Indices: 4075600--4075859 Score: 368
Period size: 57 Copynumber: 4.5 Consensus size: 57
4075590 GATTTTCAAG
*
4075600 TTTCAACTTTTCTTCAAAAACCTTTTTTTGAAATTTATTTTTAAGAAAAATTGATAC
1 TTTCAACTTTTCTCCAAAAACCTTTTTTTGAAATTTATTTTTAAGAAAAATTGATAC
*
4075657 TTTCAACTTTTCTTC-AAAACCTTTTTTTTGAAATTTATTTTTAAGAAAAATTGATAC
1 TTTCAACTTTTCTCCAAAAACC-TTTTTTTGAAATTTATTTTTAAGAAAAATTGATAC
*
4075714 TTTCAACTTTTCTCCAAAAA--TATTTTTTGAAAACTTTGATTTTTAAGGAAAATTGATAC
1 TTTCAACTTTTCTCCAAAAACCT-TTTTTTG-AAA-TTT-ATTTTTAAGAAAAATTGATAC
4075773 TTTCAACTTTTC-CTCAAAAACCTTTTTTTGAAATTTTATTTTTAAGAAAAATTGATAC
1 TTTCAACTTTTCTC-CAAAAACCTTTTTTTGAAA-TTTATTTTTAAGAAAAATTGATAC
**
4075831 TTTCAACTTTT-TCCCAAAAATATTTTTTT
1 TTTCAACTTTTCT-CCAAAAACCTTTTTTT
4075860 TGGATTTTAT
Statistics
Matches: 186, Mismatches: 6, Indels: 21
0.87 0.03 0.10
Matches are distributed among these distances:
55 1 0.01
56 13 0.07
57 67 0.36
58 52 0.28
59 45 0.24
60 7 0.04
61 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.48
Consensus pattern (57 bp):
TTTCAACTTTTCTCCAAAAACCTTTTTTTGAAATTTATTTTTAAGAAAAATTGATAC
Found at i:4075840 original size:117 final size:113
Alignment explanation
Indices: 4075600--4075858 Score: 398
Period size: 117 Copynumber: 2.2 Consensus size: 113
4075590 GATTTTCAAG
*
4075600 TTTCAACTTTTCTTCAAAAACCT-TTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAAC
1 TTTCAACTTTTCTCCAAAAA--TATTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAAC
*
4075664 TTTTCTTCAAAACCTTTTTTTTGAAATTTATTTTTAAGAAAAATTGATAC
64 TTTTCCTCAAAACCTTTTTTTTGAAATTTATTTTTAAGAAAAATTGATAC
*
4075714 TTTCAACTTTTCTCCAAAAATATTTTTTGAAAACTTTGATTTTTAAGGAAAATTGATACTTTCAA
1 TTTCAACTTTTCTCCAAAAATATTTTTTG-AAA-TTT-ATTTTTAAGAAAAATTGATACTTTCAA
4075779 CTTTTCCTCAAAAACC-TTTTTTTGAAATTTTATTTTTAAGAAAAATTGATAC
63 CTTTTCCTC-AAAACCTTTTTTTTGAAA-TTTATTTTTAAGAAAAATTGATAC
4075831 TTTCAACTTTT-TCCCAAAAATATTTTTT
1 TTTCAACTTTTCT-CCAAAAATATTTTTT
4075859 TTGGATTTTA
Statistics
Matches: 135, Mismatches: 3, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
112 1 0.01
113 7 0.05
114 22 0.16
115 3 0.02
116 46 0.34
117 56 0.41
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (113 bp):
TTTCAACTTTTCTCCAAAAATATTTTTTGAAATTTATTTTTAAGAAAAATTGATACTTTCAACTT
TTCCTCAAAACCTTTTTTTTGAAATTTATTTTTAAGAAAAATTGATAC
Found at i:4075884 original size:5 final size:5
Alignment explanation
Indices: 4075876--4075951 Score: 50
Period size: 5 Copynumber: 14.8 Consensus size: 5
4075866 TTATTTAAAG
* * *
4075876 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AAAGT AAAACA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAA-T
*
4075926 AAAAT AAAAAT AAAAT GAAGAT AAAA
1 AAAAT -AAAAT AAAAT -AAAAT AAAA
4075952 GAACATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
3 3 0.05
4 3 0.05
5 30 0.55
6 15 0.27
7 4 0.07
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:4075926 original size:31 final size:31
Alignment explanation
Indices: 4075875--4075934 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 31
4075865 TTTATTTAAA
*
4075875 GAAAATAAAATAATAAAAC-AAAATAAAAGT
1 GAAAATAAAAAAATAAAACAAAAATAAAAGT
4075905 GAAAATAAAAAAAGTAAAACAAAAATAAAA
1 GAAAATAAAAAAA-TAAAACAAAAATAAAA
4075935 ATAAAATGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 12 0.44
31 6 0.22
32 9 0.33
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (31 bp):
GAAAATAAAAAAATAAAACAAAAATAAAAGT
Found at i:4075941 original size:31 final size:30
Alignment explanation
Indices: 4075875--4075941 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
4075865 TTTATTTAAA
* *
4075875 GAAAATAAAATAATAAAACAAAATAAAAGT
1 GAAAATAAAAAAATAAAACAAAATAAAAAT
4075905 GAAAATAAAAAAAGTAAAACAAAAATAAAAAT
1 GAAAATAAAAAAA-TAAAAC-AAAATAAAAAT
4075937 -AAAAT
1 GAAAAT
4075942 GAAGATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 12 0.36
31 11 0.33
32 10 0.30
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (30 bp):
GAAAATAAAAAAATAAAACAAAATAAAAAT
Found at i:4076870 original size:19 final size:19
Alignment explanation
Indices: 4076846--4076892 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
4076836 CCAAAAAAAA
*
4076846 AAAAAAAATCAGATAAACG
1 AAAAAAAATAAGATAAACG
4076865 AAAAAAAATAAGATAAACG
1 AAAAAAAATAAGATAAACG
4076884 AATAAAAAA
1 AA-AAAAAA
4076893 ATTAACAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.11
Consensus pattern (19 bp):
AAAAAAAATAAGATAAACG
Found at i:4076911 original size:40 final size:43
Alignment explanation
Indices: 4076867--4076963 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
4076857 GATAAACGAA
* *
4076867 AAAAAATAA-GATAA-ACGAATAAAAAA-ATTA-ACAGAT-AAT
1 AAAAAATAATAATAAGACAAATAAAAAATATTACA-AGATAAAT
* *
4076906 TAAAAATAATAATAAGATAAATAAAAAATATTACAAGATAAAT
1 AAAAAATAATAATAAGACAAATAAAAAATATTACAAGATAAAT
4076949 AAAAAATAATAATAA
1 AAAAAATAATAATAA
4076964 TAATAAATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
39 8 0.17
40 4 0.08
41 10 0.21
42 8 0.17
43 18 0.38
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (43 bp):
AAAAAATAATAATAAGACAAATAAAAAATATTACAAGATAAAT
Found at i:4076911 original size:42 final size:43
Alignment explanation
Indices: 4076856--4076960 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 43
4076846 AAAAAAAATC
* *
4076856 AGATAAACGAAAAAAAATAAGATAA-ACGAATAAAAAA-ATTA-A
1 AGATAAA-TAAAAAAAATAA-ATAAGACAAATAAAAAATATTACA
* * *
4076898 CAGATAATTAAAAATAAT-AATAAGATAAATAAAAAATATTACA
1 -AGATAAATAAAAAAAATAAATAAGACAAATAAAAAATATTACA
4076941 AGATAAATAAAAAATAATAA
1 AGATAAATAAAAAA-AATAA
4076961 TAATAATAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
40 4 0.08
41 11 0.22
42 24 0.48
43 10 0.20
44 1 0.02
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (43 bp):
AGATAAATAAAAAAAATAAATAAGACAAATAAAAAATATTACA
Found at i:4076955 original size:21 final size:20
Alignment explanation
Indices: 4076884--4077013 Score: 83
Period size: 21 Copynumber: 6.3 Consensus size: 20
4076874 AAGATAAACG
4076884 AATAAAAAA-ATTAACAGAT-
1 AATAAAAAATATTAA-AGATA
* *
4076903 AATTAAAAATAATAATAAGATA
1 AATAAAAAAT-ATTA-AAGATA
4076925 AATAAAAAATATTACAAGATA
1 AATAAAAAATATTA-AAGATA
*
4076946 AATAAAAAATAATAATA-AT-
1 AATAAAAAATATTAA-AGATA
* *
4076965 AATAAATAA-ATTATA-ATA
1 AATAAAAAATATTAAAGATA
*
4076983 TAATAATAAATATATAACTAGATA
1 -AATAAAAAATAT-TAA--AGATA
4077007 AATAAAA
1 AATAAAA
4077014 TACATATATA
Statistics
Matches: 86, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
17 3 0.03
18 3 0.03
19 23 0.27
20 5 0.06
21 32 0.37
22 10 0.12
23 7 0.08
24 3 0.03
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (20 bp):
AATAAAAAATATTAAAGATA
Found at i:4076966 original size:37 final size:42
Alignment explanation
Indices: 4076884--4076974 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 42
4076874 AAGATAAACG
*
4076884 AATAAAAAA-ATTAACAGATAATTAAAAATAATAATAAGATA
1 AATAAAAAATATTAACAGATAAATAAAAATAATAATAAGATA
*
4076925 AATAAAAAATATT-ACAAGATAAATAAAAAATAATAATAATAATA
1 AATAAAAAATATTAAC-AGATAAAT-AAAAATAATAATAA-GATA
4076969 AATAAA
1 AATAAA
4076975 TTATAATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 11 0.25
42 10 0.23
43 14 0.32
44 9 0.20
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (42 bp):
AATAAAAAATATTAACAGATAAATAAAAATAATAATAAGATA
Found at i:4076969 original size:40 final size:42
Alignment explanation
Indices: 4076884--4077013 Score: 123
Period size: 41 Copynumber: 3.2 Consensus size: 42
4076874 AAGATAAACG
*
4076884 AATAAAAAA-ATTAACAGATAATTAAAAATAATAATAAGATA
1 AATAAAAAATATTAACAGATAATAAAAAATAATAATAAGATA
4076925 AATAAAAAATATT-ACAAGATAAATAAAAAATAATAAT-A-AT-
1 AATAAAAAATATTAAC-AGAT-AATAAAAAATAATAATAAGATA
* * *
4076965 AATAAATAA-ATTATA-ATATAATAATAAATATATAACT-AGATA
1 AATAAAAAATATTA-ACAGATAATAAAAAATA-ATAA-TAAGATA
4077007 AATAAAA
1 AATAAAA
4077014 TACATATATA
Statistics
Matches: 75, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
38 10 0.13
39 10 0.13
40 10 0.13
41 16 0.21
42 14 0.19
43 15 0.20
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (42 bp):
AATAAAAAATATTAACAGATAATAAAAAATAATAATAAGATA
Found at i:4076974 original size:4 final size:4
Alignment explanation
Indices: 4076916--4077158 Score: 86
Period size: 4 Copynumber: 61.5 Consensus size: 4
4076906 TAAAAATAAT
* *
4076916 AATA AGATA AATA AA-A AATA TTACA AGATA AATA AA-A AAT- AAT- AAT-
1 AATA A-ATA AATA AATA AATA -AATA A-ATA AATA AATA AATA AATA AATA
* * *
4076962 AAT- AATA AATA AATTA TAATA TAAT- AATA AATA TATA ACTA GATA AATAA
1 AATA AATA AATA AA-TA -AATA -AATA AATA AATA AATA AATA AATA AAT-A
* * * * *
4077012 AATA CATA TATA AAT- ATTA ACA-A AATA AATA AATA AATA AAGA TATA
1 AATA AATA AATA AATA AATA A-ATA AATA AATA AATA AATA AATA AATA
* * * * *
4077059 CATA TATT AATA CATA GTAAT- AATA AATA AATA AAT- AATA AATA CATAA
1 AATA AATA AATA AATA --AATA AATA AATA AATA AATA AATA AATA AAT-A
* ** *
4077108 AATA CA-A AGGA AAAA AATA AA-A TAA-A AATA AA-A AATA AA-A AATA
1 AATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA AATA AATA
4077152 ATATA AA
1 A-ATA AA
4077159 ATACAAAATA
Statistics
Matches: 182, Mismatches: 33, Indels: 48
0.69 0.13 0.18
Matches are distributed among these distances:
3 40 0.22
4 110 0.60
5 28 0.15
6 4 0.02
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:4076988 original size:22 final size:23
Alignment explanation
Indices: 4076907--4077169 Score: 113
Period size: 23 Copynumber: 11.3 Consensus size: 23
4076897 ACAGATAATT
*
4076907 AAAAATAATAATAA-GATAAATA
1 AAAAATAATAATAATAATAAATA
* * *
4076929 AAAAAT-ATTACAA-GATAAATA
1 AAAAATAATAATAATAATAAATA
4076950 AAAAATAATAATAATAATAAATA
1 AAAAATAATAATAATAATAAATA
**
4076973 AATTATAAT-ATAATAATAAATA
1 AAAAATAATAATAATAATAAATA
* * *
4076995 TATAACTAGATAAATAA-AATACATA
1 -AAAAATA-AT-AATAATAATAAATA
* * *
4077020 TATAAATATTAACAA-AATAAATA
1 -AAAAATAATAATAATAATAAATA
*
4077043 AATAAATAA-AGAT-ATACATATATTA
1 AA-AAATAATA-ATAATA-ATA-AATA
* * *
4077068 ATACATAGTAATAATAAATAAATA
1 AAAAATAATAATAAT-AATAAATA
*
4077092 AATAATAAATACATAA-AATACAA-A
1 AAAAAT-AATA-ATAATAATA-AATA
4077116 GGAAAAA-AATAA-AATAA-AAATA
1 --AAAAATAATAATAATAATAAATA
*
4077138 AAAAATAAAAAATAAT-ATAAAATA
1 AAAAAT-AATAATAATAAT-AAATA
*
4077162 CAAAATAA
1 AAAAATAA
4077170 AAGTCAAATT
Statistics
Matches: 184, Mismatches: 31, Indels: 51
0.69 0.12 0.19
Matches are distributed among these distances:
20 5 0.03
21 21 0.11
22 36 0.20
23 43 0.23
24 37 0.20
25 29 0.16
26 13 0.07
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.25
Consensus pattern (23 bp):
AAAAATAATAATAATAATAAATA
Found at i:4077127 original size:20 final size:18
Alignment explanation
Indices: 4077077--4077171 Score: 70
Period size: 19 Copynumber: 5.1 Consensus size: 18
4077067 AATACATAGT
*
4077077 AATAATAAAT-AAATAAA
1 AATAAAAAATAAAATAAA
*
4077094 TAATAAATACATAAAATACAA
1 -AATAAA-AAATAAAATA-AA
4077115 AGGA-AAAAAATAAAATAAA
1 A--ATAAAAAATAAAATAAA
4077134 AATAAAAAATAAAA-AATA
1 AATAAAAAATAAAATAA-A
* *
4077152 ATATAAAATACAAAATAAA
1 A-ATAAAAAATAAAATAAA
4077171 A
1 A
4077172 GTCAAATTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
17 3 0.05
18 18 0.29
19 19 0.30
20 17 0.27
21 5 0.08
22 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (18 bp):
AATAAAAAATAAAATAAA
Found at i:4077166 original size:24 final size:24
Alignment explanation
Indices: 4077091--4077171 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 24
4077081 ATAAATAAAT
* *
4077091 AAATAATAAAT-ACATAAAATACA
1 AAATAAAAAATAAAATAAAATACA
*
4077114 AAGGA-AAAAAATAAAATAAAAATAAA
1 AA--ATAAAAAATAAAAT-AAAATACA
*
4077140 AAATAAAAAATAATATAAAATACA
1 AAATAAAAAATAAAATAAAATACA
4077164 AAATAAAA
1 AAATAAAA
4077172 GTCAAATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.04
24 22 0.46
25 15 0.31
26 9 0.19
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (24 bp):
AAATAAAAAATAAAATAAAATACA
Found at i:4077670 original size:38 final size:39
Alignment explanation
Indices: 4077593--4077672 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 39
4077583 TCTCCTGGAA
4077593 ATATACATACATGCTAAGTCAAAGCTAAAGAATCCATAGG
1 ATATACATACATGCTAAG-CAAAGCTAAAGAATCCATAGG
**
4077633 ATATACATACATGCTAAG-AAAGCTAAAGAATTTATAGG
1 ATATACATACATGCTAAGCAAAGCTAAAGAATCCATAGG
4077671 AT
1 AT
4077673 CCCTCTTTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 20 0.53
40 18 0.47
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (39 bp):
ATATACATACATGCTAAGCAAAGCTAAAGAATCCATAGG
Found at i:4087160 original size:21 final size:20
Alignment explanation
Indices: 4087135--4087178 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
4087125 TGAACTTTAA
*
4087135 AAAATTCTCAAAATTATATCT
1 AAAATTATCAAAATTATAT-T
* *
4087156 AAAATTATTAAAATTTTATT
1 AAAATTATCAAAATTATATT
4087176 AAA
1 AAA
4087179 CTTTTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATTATCAAAATTATATT
Found at i:4087272 original size:21 final size:19
Alignment explanation
Indices: 4087248--4087351 Score: 64
Period size: 21 Copynumber: 4.9 Consensus size: 19
4087238 TTTGTTGAAA
4087248 TTTATTAAAAATTATCAAATT
1 TTTA-TAAAAATTATCAAA-T
*
4087269 TTTATAGAAAGTTATCAAAT
1 TTTATA-AAAATTATCAAAT
* *
4087289 TTTAATAAAAATAAGTTATAAAAA
1 TTT-AT--AAA-AA-TTATCAAAT
* *
4087313 ATTATAAAAATTAATAAAAT
1 TTTATAAAAATT-ATCAAAT
*
4087333 TTTATTAAAAATGATCAAA
1 TTTA-TAAAAATTATCAAA
4087352 ATCATATTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.03
20 22 0.33
21 27 0.41
22 2 0.03
23 4 0.06
24 9 0.14
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (19 bp):
TTTATAAAAATTATCAAAT
Found at i:4093579 original size:17 final size:16
Alignment explanation
Indices: 4093559--4093592 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4093549 TATAAATTTA
4093559 ATTTATCTATAACTTAT
1 ATTTATCTATAA-TTAT
*
4093576 ATTTATTTATAATTAT
1 ATTTATCTATAATTAT
4093592 A
1 A
4093593 GTGAATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTATCTATAATTAT
Found at i:4098808 original size:30 final size:30
Alignment explanation
Indices: 4098772--4098829 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
4098762 TGATCCAAAT
4098772 ATATATATATATATAGAGAGAGAGAGAGAG
1 ATATATATATATATAGAGAGAGAGAGAGAG
4098802 ATATATATATATATAGAGAGAGAGAGAG
1 ATATATATATATATAGAGAGAGAGAGAG
4098830 CATGAGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (30 bp):
ATATATATATATATAGAGAGAGAGAGAGAG
Found at i:4099630 original size:2 final size:2
Alignment explanation
Indices: 4099625--4099649 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4099615 TCTGTGTGTG
4099625 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4099650 GTATGTATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4100521 original size:2 final size:2
Alignment explanation
Indices: 4100514--4100538 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4100504 TCACATACGC
4100514 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4100539 GTTTTTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4104082 original size:10 final size:10
Alignment explanation
Indices: 4104053--4104086 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
4104043 GTCTGATGAT
4104053 ATTAATAATA
1 ATTAATAATA
4104063 A-TAATAATA
1 ATTAATAATA
*
4104072 ATTAATTATA
1 ATTAATAATA
4104082 ATTAA
1 ATTAA
4104087 AAAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTAATAATA
Found at i:4106406 original size:29 final size:28
Alignment explanation
Indices: 4106373--4106427 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
4106363 TTATAAATTA
* *
4106373 ATAATTATTTAAATATTTAATATTTTATT
1 ATAATTAATCAAATATTTAAT-TTTTATT
*
4106402 ATAATTAATCAAATTTTTAATTTTTA
1 ATAATTAATCAAATATTTAATTTTTA
4106428 ATTTGATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
ATAATTAATCAAATATTTAATTTTTATT
Found at i:4109251 original size:17 final size:16
Alignment explanation
Indices: 4109229--4109272 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
4109219 TAAATATGGG
4109229 TATAAAAATAAATATAA
1 TATAAAAATAAA-ATAA
*
4109246 TATAAAAAT-TAATAA
1 TATAAAAATAAAATAA
4109261 -ATAAAAATAAAA
1 TATAAAAATAAAA
4109273 GATATTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 1 0.04
17 9 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TATAAAAATAAAATAA
Found at i:4112830 original size:134 final size:134
Alignment explanation
Indices: 4112583--4112894 Score: 289
Period size: 134 Copynumber: 2.3 Consensus size: 134
4112573 TTTTATATTT
* * *
4112583 TTTTAACTTTTTTCTTTTTTTAAATATTTAATAAATATTTTCTAAAATTATAAAAATAACTTTTT
1 TTTTAACTTTGTCCTTTTTTAAAATATTTAATAAATATTTTCTAAAATTATAAAAATAACTTTTT
* *** *
4112648 AAAGATTTTATTTTTTATACATGGAATCCACTTATATCATTTTTTTTTTTTTGCTTCTCTTTGTT
66 AAAGATTTTATTTTTTATACATGGAATCCACTTAAATCAAAATCTTTTTTTTGCTTCTCTTTGTT
4112713 ATCC
131 ATCC
* **
4112717 TTTTAACTTTGTCCGTTTATTTAAAACTATTTAAT-AATATTTT-TTAAATTATAAATTTATA-T
1 TTTTAACTTTGTCC-TTT-TTTAAAA-TATTTAATAAATATTTTCTAAAATTATAAAAATA-ACT
*** * *
4112779 TTCTT-AAG-TTTTATTTTTTATGTGTGGAATCCACTTAAATTAAAATC--TTTTTTGCTTTTTC
62 TT-TTAAAGATTTTATTTTTTATACATGGAATCCACTTAAATCAAAATCTTTTTTTTGC-TTCTC
*
4112840 TTT-TTACCC
125 TTTGTTATCC
* * * * *
4112849 TTTTTAATTTTTTTCTTTTTAAAAAGTATTTAATGAAAAATTTTCT
1 -TTTTAACTTTGTCCTTTTTTAAAA-TATTTAAT-AAATATTTTCT
4112895 GATTTAATAT
Statistics
Matches: 145, Mismatches: 23, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
131 14 0.10
132 16 0.11
133 25 0.17
134 43 0.30
135 22 0.15
136 17 0.12
137 8 0.06
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (134 bp):
TTTTAACTTTGTCCTTTTTTAAAATATTTAATAAATATTTTCTAAAATTATAAAAATAACTTTTT
AAAGATTTTATTTTTTATACATGGAATCCACTTAAATCAAAATCTTTTTTTTGCTTCTCTTTGTT
ATCC
Found at i:4113066 original size:22 final size:21
Alignment explanation
Indices: 4113041--4113099 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4113031 AAGTCATTTG
4113041 GCTTTTTTTTTTTTTCACTTTT
1 GCTTTTTTTTTTTTT-ACTTTT
* *
4113063 GCTTCTTTTTTATTTACTTTT
1 GCTTTTTTTTTTTTTACTTTT
* *
4113084 GCATTTTTTCTTTTTA
1 GCTTTTTTTTTTTTTA
4113100 AAAAATATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.08, C:0.14, G:0.05, T:0.73
Consensus pattern (21 bp):
GCTTTTTTTTTTTTTACTTTT
Found at i:4113119 original size:19 final size:21
Alignment explanation
Indices: 4113095--4113139 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4113085 CATTTTTTCT
*
4113095 TTTTAAAAA-AT-ATTTAATA
1 TTTTAAAAATATAATATAATA
4113114 TTTTAAAAATATAATATAATA
1 TTTTAAAAATATAATATAATA
4113135 TTTTA
1 TTTTA
4113140 TTTAATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAAATATAATATAATA
Found at i:4113490 original size:15 final size:16
Alignment explanation
Indices: 4113462--4113499 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
4113452 TACTTTCACA
*
4113462 TTTTTCTATATTTTTTC
1 TTTTTCTAT-TTTTATC
4113479 TTTTTCTATTTTTATC
1 TTTTTCTATTTTTATC
4113495 TTTTT
1 TTTTT
4113500 AATATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCTATTTTTATC
Found at i:4114133 original size:57 final size:59
Alignment explanation
Indices: 4114006--4114163 Score: 241
Period size: 57 Copynumber: 2.7 Consensus size: 59
4113996 TTTTTTTTAG
*
4114006 GGAAAATTGATACTTTCAACTTTTCCCAAAAAAATATTTTTTTGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAAATATTTTTTGGAAATTTTGATTTTCAA
* *
4114066 GGAAAATTGATACTTTCAACTCTTCCCCAAAAATATTTTTTGGAAA-TTT-A-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTGGAAATTTTGATTTTC-AA
*
4114123 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTT
4114164 TTTGGAATTT
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
56 4 0.04
57 42 0.46
58 3 0.03
59 17 0.18
60 26 0.28
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.42
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTGGAAATTTTGATTTTCAA
Found at i:4115248 original size:14 final size:16
Alignment explanation
Indices: 4115218--4115251 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
4115208 TAGATAAGTA
4115218 AAAATACAAAAATGAT
1 AAAATACAAAAATGAT
4115234 AAAATA-AAAAA-GAT
1 AAAATACAAAAATGAT
4115248 AAAA
1 AAAA
4115252 AATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 5 0.28
16 6 0.33
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAATACAAAAATGAT
Found at i:4115255 original size:16 final size:17
Alignment explanation
Indices: 4115216--4115252 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
4115206 ATTAGATAAG
4115216 TAAAAATACAAAAATGA
1 TAAAAATACAAAAATGA
4115233 T-AAAATA-AAAAA-GA
1 TAAAAATACAAAAATGA
4115247 TAAAAA
1 TAAAAA
4115253 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 9 0.47
16 6 0.32
17 1 0.05
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
TAAAAATACAAAAATGA
Found at i:4119136 original size:2 final size:2
Alignment explanation
Indices: 4119129--4119155 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4119119 TTCGCTCTGC
4119129 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
4119156 GCCCCACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4124503 original size:66 final size:66
Alignment explanation
Indices: 4124351--4124508 Score: 165
Period size: 66 Copynumber: 2.4 Consensus size: 66
4124341 AAAAACCTAG
* * * * * * *
4124351 ACCGAAAGTCAAAAAAATAAAATAACTTAGATTGAGCTGAAGTCGAAAATGAGTGATTGGGATTA
1 ACCGCAAGTCAAAAAAATAAAATGACATAGATTGAGCTCAAGACGAAAATGAGTGATCGAGATTA
4124416 A
66 A
* * * * * *
4124417 ATCGCAAGTTAGAAATATAAAATGACATGGATTGAGC-CAAGGACGAACATGAGTGATCGAGATT
1 ACCGCAAGTCAAAAAAATAAAATGACATAGATTGAGCTCAA-GACGAAAATGAGTGATCGAGATT
*
4124481 GA
65 AA
*
4124483 ACCGCATGTCAAAAAAATAAAATGAC
1 ACCGCAAGTCAAAAAAATAAAATGAC
4124509 TTGAACTGAA
Statistics
Matches: 72, Mismatches: 19, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
65 2 0.03
66 70 0.97
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.21
Consensus pattern (66 bp):
ACCGCAAGTCAAAAAAATAAAATGACATAGATTGAGCTCAAGACGAAAATGAGTGATCGAGATTA
A
Found at i:4137096 original size:3 final size:3
Alignment explanation
Indices: 4137088--4137113 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4137078 TTTCTTTCTT
4137088 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4137114 TGTTTAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4141321 original size:20 final size:20
Alignment explanation
Indices: 4141296--4141348 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
4141286 ATATAATATT
* **
4141296 TATAAAATATTACTTTTTTA
1 TATAAAATATAACTTAATTA
*
4141316 TATAAATTATAACTTAATTA
1 TATAAAATATAACTTAATTA
4141336 TATATAAATATAA
1 TATA-AAATATAA
4141349 TATTTTTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
TATAAAATATAACTTAATTA
Found at i:4141404 original size:22 final size:23
Alignment explanation
Indices: 4141332--4141414 Score: 66
Period size: 22 Copynumber: 3.7 Consensus size: 23
4141322 TTATAACTTA
* *
4141332 ATTATATATAAATATAATATTTTT
1 ATTA-ATATTAATATAATAATTTT
* *
4141356 GTTAA-ATTAATATATTAA-TTT
1 ATTAATATTAATATAATAATTTT
*
4141377 A-AAATATTAA-ATAATAATTTT
1 ATTAATATTAATATAATAATTTT
*
4141398 ATTAATAATATATATAA
1 ATTAATATTA-ATATAA
4141415 ATATAAAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
20 8 0.18
21 12 0.27
22 16 0.36
23 2 0.04
24 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
ATTAATATTAATATAATAATTTT
Found at i:4143536 original size:21 final size:22
Alignment explanation
Indices: 4143512--4143565 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
4143502 ATCATATCTC
4143512 TTTCTCTTCATCTTTC-CTTTA
1 TTTCTCTTCATCTTTCTCTTTA
* * *
4143533 TTTCTCTTTATTTTTCTTTTTA
1 TTTCTCTTCATCTTTCTCTTTA
*
4143555 TTTTTCTTCAT
1 TTTCTCTTCAT
4143566 TTATTTCTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTCTCTTCATCTTTCTCTTTA
Found at i:4143554 original size:12 final size:12
Alignment explanation
Indices: 4143533--4143562 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4143523 CTTTCCTTTA
*
4143533 TTTCTCTTTATT
1 TTTCTTTTTATT
4143545 TTTCTTTTTATT
1 TTTCTTTTTATT
4143557 TTTCTT
1 TTTCTT
4143563 CATTTATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTCTTTTTATT
Found at i:4144620 original size:40 final size:40
Alignment explanation
Indices: 4144565--4144645 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
4144555 ACGGTAGTCG
*
4144565 ATAAGAGGTGTTGGGATTTTAAAGAGAAAGGCTCTAGGGT
1 ATAAGAGGTGCTGGGATTTTAAAGAGAAAGGCTCTAGGGT
* *
4144605 ATAAGAGGTGCTGGGATTTTAGAGAGAAAGGCTCTATGGT
1 ATAAGAGGTGCTGGGATTTTAAAGAGAAAGGCTCTAGGGT
4144645 A
1 A
4144646 GAAAGAGAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.27
Consensus pattern (40 bp):
ATAAGAGGTGCTGGGATTTTAAAGAGAAAGGCTCTAGGGT
Found at i:4144857 original size:12 final size:12
Alignment explanation
Indices: 4144809--4144853 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
4144799 CTTTTTTGTT
* *
4144809 TTGATTTTGATT
1 TTGATTTTTATG
4144821 TTGATATTTTATG
1 TTGAT-TTTTATG
4144834 TTGATTTTTATG
1 TTGATTTTTATG
4144846 TT-ATTTTT
1 TTGATTTTT
4144854 TATGATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 6 0.20
12 14 0.47
13 10 0.33
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (12 bp):
TTGATTTTTATG
Found at i:4144869 original size:3 final size:3
Alignment explanation
Indices: 4144861--4144914 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
4144851 TTTTATGATG
4144861 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4144909 TTA TTA
1 TTA TTA
4144915 CTGGTAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4145125 original size:22 final size:22
Alignment explanation
Indices: 4145091--4145143 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4145081 TGGGATAATT
**
4145091 TAAAAAAAT-AATTTTG-TAAA
1 TAAAAAAATAAAAATTGATAAA
4145111 -AAAAAAATAAAAATTGATAAA
1 TAAAAAAATAAAAATTGATAAA
4145132 TAAAAAAATAAA
1 TAAAAAAATAAA
4145144 TTGTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.29
20 5 0.18
21 4 0.14
22 11 0.39
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (22 bp):
TAAAAAAATAAAAATTGATAAA
Found at i:4145136 original size:20 final size:21
Alignment explanation
Indices: 4145091--4145156 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
4145081 TGGGATAATT
*
4145091 TAAAAAAATAATTTTGTA-AAA
1 TAAAAAAATAA-ATTGTATAAA
*
4145112 -AAAAAATAAAAATTG-ATAAA
1 TAAAAAA-ATAAATTGTATAAA
*
4145132 TAAAAAAATAAATTGTTTAAA
1 TAAAAAAATAAATTGTATAAA
4145153 TAAA
1 TAAA
4145157 TATTTTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.03
20 19 0.51
21 17 0.46
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
TAAAAAAATAAATTGTATAAA
Found at i:4145152 original size:21 final size:21
Alignment explanation
Indices: 4145091--4145156 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
4145081 TGGGATAATT
4145091 TAAAAAAAT-AATT-TTGTAAA
1 TAAAAAAATAAATTGTT-TAAA
*
4145111 -AAAAAAATAAAAATTG-ATAAA
1 TAAAAAAAT--AAATTGTTTAAA
4145132 TAAAAAAATAAATTGTTTAAA
1 TAAAAAAATAAATTGTTTAAA
4145153 TAAA
1 TAAA
4145157 TATTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
19 8 0.21
20 6 0.16
21 12 0.32
22 12 0.32
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (21 bp):
TAAAAAAATAAATTGTTTAAA
Found at i:4145338 original size:16 final size:13
Alignment explanation
Indices: 4145302--4145343 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
4145292 TAAACAATGT
4145302 AAAATAATAATAA
1 AAAATAATAATAA
4145315 AAAATAATAATAA
1 AAAATAATAATAA
4145328 ATGAAATTAATAATAA
1 A--AAA-TAATAATAA
4145344 TTGATATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.54
15 3 0.12
16 9 0.35
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:4145520 original size:38 final size:39
Alignment explanation
Indices: 4145457--4145535 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 39
4145447 ATTTAAAATT
4145457 TTTTTTATAAAAAAATATAATTAAAGAATAAATAATAAA
1 TTTTTTATAAAAAAATATAATTAAAGAATAAATAATAAA
* * * *
4145496 TTTTTTA-AAAATAATCATAA-TAAAGATTAATTAATTAA
1 TTTTTTATAAAAAAAT-ATAATTAAAGAATAAATAATAAA
4145534 TT
1 TT
4145536 CCTTTAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 24 0.69
39 11 0.31
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.41
Consensus pattern (39 bp):
TTTTTTATAAAAAAATATAATTAAAGAATAAATAATAAA
Found at i:4147533 original size:34 final size:34
Alignment explanation
Indices: 4147488--4147568 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
4147478 AAAACTCTGC
* * *
4147488 CTACAACTAAGATGCAATTAGCAGGAACAAAATG
1 CTACAATTAAGATGCAATTAACAGGAACAAAATA
* * *
4147522 CTACAATTAAGATGTAATTAATAGGAATAAAATA
1 CTACAATTAAGATGCAATTAACAGGAACAAAATA
4147556 CTACAATTAAGAT
1 CTACAATTAAGAT
4147569 TAAGGAAGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (34 bp):
CTACAATTAAGATGCAATTAACAGGAACAAAATA
Found at i:4161385 original size:3 final size:3
Alignment explanation
Indices: 4161370--4161400 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
4161360 TTTTGAAATA
*
4161370 AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4161401 GTAAAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4165076 original size:41 final size:42
Alignment explanation
Indices: 4165018--4165102 Score: 145
Period size: 41 Copynumber: 2.0 Consensus size: 42
4165008 TTAAGTAAAG
*
4165018 TTAGTTTCTGTCCTGAGGTGAATTTCAATTCAACCGTT-CTT
1 TTAGTTTCTATCCTGAGGTGAATTTCAATTCAACCGTTCCTT
*
4165059 TTAGTTTCTATCTTGAGGTGAATTTCAATTCAACCGTTCCTT
1 TTAGTTTCTATCCTGAGGTGAATTTCAATTCAACCGTTCCTT
4165101 TT
1 TT
4165103 CCAATCACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 36 0.88
42 5 0.12
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.46
Consensus pattern (42 bp):
TTAGTTTCTATCCTGAGGTGAATTTCAATTCAACCGTTCCTT
Found at i:4173927 original size:114 final size:114
Alignment explanation
Indices: 4173726--4173938 Score: 304
Period size: 114 Copynumber: 1.9 Consensus size: 114
4173716 AGGTAGGCAG
* * *
4173726 GGTGGCCAACCTCCGTGACAAGAGCGTCACGAGATTAGGTAGGGGAGAATGTCACAGACCTAAAG
1 GGTGGCCAACCTCCATGACAAGAGCGTCACGAAATTAGGTAGGGGAAAATGTCACAGACCTAAAG
*
4173791 AGGAGTTCTGAATCCTAAATCGAATATAAAAGAAAGGTGGCCTCGGTAA
66 AAGAGTTCTGAATCCTAAATCGAATATAAAAGAAAGGTGGCCTCGGTAA
** * * *
4173840 GGTGGCCAACCTCCATGATGAGGGCGTCACGAAATTAGGT-GGGAGAAAATGTCACGGACTTAAA
1 GGTGGCCAACCTCCATGACAAGAGCGTCACGAAATTAGGTAGGG-GAAAATGTCACAGACCTAAA
*
4173904 GAAGAG-TCTTGAATCCTATATCGAATATAAAAGAA
65 GAAGAGTTC-TGAATCCTAAATCGAATATAAAAGAA
4173939 GAGTAATTGG
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
113 5 0.06
114 82 0.94
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (114 bp):
GGTGGCCAACCTCCATGACAAGAGCGTCACGAAATTAGGTAGGGGAAAATGTCACAGACCTAAAG
AAGAGTTCTGAATCCTAAATCGAATATAAAAGAAAGGTGGCCTCGGTAA
Found at i:4189789 original size:5 final size:5
Alignment explanation
Indices: 4189775--4189930 Score: 77
Period size: 5 Copynumber: 29.6 Consensus size: 5
4189765 AAATGTTCAA
* * * * *
4189775 ATTTT TTTTT ATTTT ATCTT ATTTT GTTTT ATTTT -CTTT ATAATT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT
* * * * *
4189825 GTCTTT ATTTTT ATTTC ATCTT ATCTTT GTATTT ATGTTT ATTTT A-TTC
1 AT-TTT A-TTTT ATTTT ATTTT AT-TTT AT-TTT AT-TTT ATTTT ATTTT
*
4189874 A-TTT ATCTTT ATTCT ACTTTT ATCTTT ATTCTT ATCTTT A-TTT ATTTT
1 ATTTT AT-TTT ATTTT A-TTTT AT-TTT ATT-TT AT-TTT ATTTT ATTTT
4189922 ATTATT ATT
1 ATT-TT ATT
4189931 GTTTAAAAAA
Statistics
Matches: 114, Mismatches: 24, Indels: 25
0.70 0.15 0.15
Matches are distributed among these distances:
4 13 0.11
5 50 0.44
6 49 0.43
7 2 0.02
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:4189846 original size:17 final size:16
Alignment explanation
Indices: 4189801--4189921 Score: 61
Period size: 17 Copynumber: 7.2 Consensus size: 16
4189791 TCTTATTTTG
4189801 TTTTATTT-TCTTTAT
1 TTTTATTTATCTTTAT
** *
4189816 AATTATTTTGTCTTTAT
1 TTTTA-TTTATCTTTAT
4189833 TTTTATTTCATC-TTAT
1 TTTTATTT-ATCTTTAT
*
4189849 CTTTGTATTTATGTTTATT
1 -TTT-TATTTATCTTTA-T
4189868 TTATTCATTTATCTTTA-
1 TT-TT-ATTTATCTTTAT
*
4189885 TTCTACTTTTATCTTTAT
1 TTTTA--TTTATCTTTAT
* *
4189903 TCTTATCTT-TATTTAT
1 TTTTAT-TTATCTTTAT
4189919 TTT
1 TTT
4189922 ATTATTATTG
Statistics
Matches: 81, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
15 4 0.05
16 20 0.25
17 31 0.38
18 14 0.17
19 12 0.15
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTATTTATCTTTAT
Found at i:4190169 original size:12 final size:12
Alignment explanation
Indices: 4190152--4190180 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4190142 GGAAAAACAT
4190152 AGAAAAGCAAAG
1 AGAAAAGCAAAG
4190164 AGAAAAGCAAAG
1 AGAAAAGCAAAG
4190176 -GAAAA
1 AGAAAA
4190181 TAAAAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.07, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAAGCAAAG
Found at i:4191253 original size:25 final size:26
Alignment explanation
Indices: 4191212--4191260 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
4191202 ACAATTATCT
4191212 AATGATAAGATTCTTAA-AAATTTCA
1 AATGATAAGATTCTTAAGAAATTTCA
*
4191237 AATGATAA-ATTTTTTAAGAAATTT
1 AATGATAAGA-TTCTTAAGAAATTT
4191261 TTAGTTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 14 0.67
26 6 0.29
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (26 bp):
AATGATAAGATTCTTAAGAAATTTCA
Found at i:4191651 original size:53 final size:53
Alignment explanation
Indices: 4191591--4191698 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
4191581 ATTTCTAAGA
* * *
4191591 AAGATATTTCTAAATTTAATCC-AAATGATGAAAAATTTAGAAATGAAACTTGT
1 AAGATATTTATAAA-TTAAGCCAAAATGATGAAAAATTTAGAAATAAAACTTGT
* * *
4191644 AAGATATTTATAAATTAGGCCAAAATGGTGAAAAGTTTAGAAATAAAACTTGT
1 AAGATATTTATAAATTAAGCCAAAATGATGAAAAATTTAGAAATAAAACTTGT
4191697 AA
1 AA
4191699 AATAAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 5 0.10
53 43 0.90
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.31
Consensus pattern (53 bp):
AAGATATTTATAAATTAAGCCAAAATGATGAAAAATTTAGAAATAAAACTTGT
Done.